Compact and lightweight nine-axis motion sensors have come to be used for motion analysis in a variety of fields such as medical care, welfare, and sports. Nine-axis motion sensors include a three-axis gyroscope, a three-axis accelerometer, and a three-axis magnetometer and can estimate joint angles using the gyroscope outputs. However, the bias of the gyroscope is often unstable depending on the measurement environment and the accuracy of the gyroscope itself, causing error to accumulate in the angle obtained by integrating the gyroscope output. Although several sensor fusions have been proposed for pose estimation, such as using an accelerometer and a magnetometer, sequentially estimating and correcting the bias of the gyroscope are desirable for more accurate pose estimation. In addition, considering accelerations other than the acceleration due to gravity is important for a sensor fusion method that utilizes the accelerometer to correct the gyroscope output. Therefore, in this study, an extended Kalman filter algorithm was developed to sequentially correct both the gyroscope bias and the centrifugal and tangential acceleration of an accelerometer. The gait measurement results indicate that the proposed method successfully suppresses drift in the estimated knee joint angle over the entire measurement time of knee angle measurement during gait. The knee joint angles estimated using the proposed method were generally consistent with results obtained from an optical 3D motion analysis system. The proposed method is expected to be useful for estimating motion in medical care and welfare applications.